Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/tree.shared.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 03 Jun 2016 09:32:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/tree.shared.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,204 @@ +<tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0"> + <description>Generate a newick tree for dissimilarity among groups</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'tree.shared( + #if $input.source == "shared": + shared=$input.dist, + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.subsampling.use == "yes": + #if $input.subsampling.subsample: + subsample=$input.subsampling.subsample, + #else + subsample=T, + #end if + #if $input.subsampling.iters: + iters="$input.subsampling.iters, + #end if + #end if + #elif $input.source == "column": + column=$input.dist, + name=$input.name, + #elif $input.source == "phylip": + phylip=$input.dist, + #if $input.name: + name=$input.name, + #end if + #else + count=$input.name, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + prefix='$input.dist' && + #if $input.source == 'shared': + mv \${prefix%.dat}*.tre . && + #else + mv \${prefix%.dat}*.tre '$tre' && + #end if + mv mothur.*.logfile '$logfile' + ]]></command> + <inputs> + <conditional name="input"> + <param name="source" type="select" label="Select input format"> + <option value="shared">OTU Shared</option> + <option value="column">Pairwise Column Distance Matrix</option> + <option value="phylip">Phylip Distance Matrix</option> + <option value="count">Count file</option> + </param> + <when value="column"> + <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> + <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> + </when> + <when value="phylip"> + <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> + </when> + <when value="shared"> + <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <options> + <filter type="data_meta" ref="dist" key="labels"/> + </options> + </param> + <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> + <options> + <filter type="data_meta" ref="dist" key="groups"/> + </options> + </param> + <conditional name="subsampling"> + <param name="use" type="select" label="subsample"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> + <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="count"> + <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> + <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/> + </when> + </conditional> + <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> + <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> + <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> + <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> + <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> + <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> + <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> + <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> + <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> + <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> + <option value="hamming">hamming - Community Membership Similarity -</option> + <option value="memchi2">memchi2 - Community Membership Similarity -</option> + <option value="memchord">memchord - Community Membership Similarity -</option> + <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option> + <option value="mempearson">mempearson - Community Membership Similarity -</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + <option value="canberra">canberra - Community Structure Similarity -</option> + <option value="gower">gower - Community Structure Similarity -</option> + <option value="hellinger">hellinger - Community Structure Similarity -</option> + <option value="manhattan">manhattan - Community Structure Similarity -</option> + <option value="odum">odum - Community Structure Similarity -</option> + <option value="soergel">soergel - Community Structure Similarity -</option> + <option value="spearman">spearman - Community Structure Similarity -</option> + <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option> + <option value="structchi2">structchi2 - Community Structure Similarity -</option> + <option value="structchord">structchord - Community Structure Similarity -</option> + <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option> + <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> + <option value="structpearson">structpearson - Community Structure Similarity -</option> + <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + </param> + </inputs> + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="tre" format="mothur.tre" label="${tool.name} on ${on_string}: tre"> + <filter>input['source'] != 'shared'</filter> + </data> + <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre"> + <filter>input['source'] == 'shared'</filter> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.tre" format="mothur.tre"/> + </collection> + </outputs> + <tests> + <test><!-- test with phylip and defaults --> + <param name="source" value="phylip"/> + <param name="dist" value="env.dist"/> + <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared and subsampling --> + <param name="source" value="shared"/> + <param name="dist" value="amazon.an.shared"/> + <param name="use" value="yes"/> + <param name="calc" value="jclass"/> + <output_collection name="trefiles" count="108"> + <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared and label and group select and all calculators --> + <param name="source" value="shared"/> + <param name="dist" value="amazon.an.shared"/> + <param name="label" value="0.05,0.22,0.32"/> + <param name="groups" value="forest,pasture"/> + <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/> + <output_collection name="trefiles" count="117"> + <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with column and name file --> + <param name="source" value="column"/> + <param name="dist" value="amazon.pair.dist"/> + <param name="name" value="amazon1.names"/> + <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators + +.. _tree.shared: http://www.mothur.org/wiki/Tree.shared + +]]> + </help> + <expand macro="citations"/> +</tool>